Sun Hequan, Schneeberger Korbinian
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
Methods Mol Biol. 2015;1284:381-95. doi: 10.1007/978-1-4939-2444-8_19.
Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifically designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.
对重组突变基因组池进行全基因组重测序，可将表型性状与因果突变直接关联起来。这种分析方法称为测序定位，它通过依赖混合基因组中全基因组等位基因频率（AF）内的选择诱导模式，将经典遗传定位与下一代测序相结合。测序定位可使用诸如SHOREmap等计算工具来进行。然而，SHOREmap的早期版本并未实施标准化分析，而是专门针对特定实验设置设计的。在此，我们介绍SHOREmap（3.0版）的一种新颖且先进的实现方式的用法，包括一些新特性，如常用文件格式的文件读取器、SNP标记选择以及定位区间的稳定计算。可在shoremap.org下载SHOREmap。
